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java.lang.Objectorg.jmol.adapter.smarter.AtomSetCollection
public class AtomSetCollection
Field Summary | |
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(package private) boolean |
applySymmetryToBonds
|
(package private) int |
atomCount
|
(package private) Atom[] |
atoms
|
(package private) int[] |
atomSetAtomCounts
|
(package private) java.util.Hashtable[] |
atomSetAuxiliaryInfo
|
(package private) int[] |
atomSetBondCounts
|
(package private) java.util.Hashtable |
atomSetCollectionAuxiliaryInfo
|
(package private) java.util.Properties |
atomSetCollectionProperties
|
(package private) int |
atomSetCount
|
(package private) java.lang.String[] |
atomSetNames
|
(package private) int[] |
atomSetNumbers
|
(package private) java.util.Properties[] |
atomSetProperties
|
(package private) java.util.Hashtable |
atomSymbolicMap
|
(package private) int |
bondCount
|
(package private) int |
bondCount0
|
(package private) int |
bondIndex0
|
(package private) Bond[] |
bonds
|
(package private) javax.vecmath.Point3f[] |
cartesians
|
(package private) boolean |
checkSpecial
|
(package private) java.lang.String |
collectionName
|
(package private) int[] |
connectLast
|
(package private) int |
connectNextAtomIndex
|
(package private) int |
connectNextAtomSet
|
(package private) boolean |
coordinatesAreFractional
|
(package private) int |
currentAtomSetIndex
|
(package private) boolean |
doNormalize
|
java.lang.String |
errorMessage
|
(package private) java.lang.String |
fileTypeName
|
(package private) static int |
GLOBAL_FRACTCOORD
|
(package private) static int |
GLOBAL_latticeCells
|
(package private) static int |
GLOBAL_SYMMETRY
|
(package private) static java.lang.String[] |
globalBooleans
|
(package private) boolean |
haveMappedSerials
|
(package private) boolean |
isLatticeRange
|
(package private) boolean |
isTrajectory
|
(package private) int[] |
latticeCells
|
private boolean |
noAutoBond
|
(package private) float[] |
notionalUnitCell
|
static java.lang.String[] |
notionalUnitcellTags
|
(package private) int |
nTrajectories
|
private javax.vecmath.Point3f |
ptTemp
|
private javax.vecmath.Point3f |
ptTemp1
|
private javax.vecmath.Point3f |
ptTemp2
|
private float |
rmaxx
|
private float |
rmaxy
|
private float |
rmaxz
|
private float |
rminx
|
private float |
rminy
|
private float |
rminz
|
(package private) int |
structureCount
|
(package private) Structure[] |
structures
|
(package private) SymmetryInterface |
symmetry
|
(package private) float |
symmetryRange
|
(package private) java.util.Vector |
trajectories
|
(package private) javax.vecmath.Point3f[] |
trajectory
|
(package private) java.util.Vector |
vConnect
|
(package private) VolumeDataInterface |
vd
|
Constructor Summary | |
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AtomSetCollection(AtomSetCollection[] array)
Creates an AtomSetCollection based on an array of AtomSetCollection |
|
AtomSetCollection(java.lang.String fileTypeName)
|
|
AtomSetCollection(java.util.Vector list)
Creates an AtomSetCollection based on a Vector of AtomSetCollection or Vector (from zipped zip files) |
Method Summary | |
---|---|
void |
addAtom(Atom atom)
|
void |
addAtomWithMappedName(Atom atom)
|
void |
addAtomWithMappedSerialNumber(Atom atom)
|
void |
addBond(Bond bond)
|
void |
addConnection(int[] is)
|
Atom |
addNewAtom()
|
Bond |
addNewBond(int atomIndex1,
int atomIndex2)
|
Bond |
addNewBond(int atomIndex1,
int atomIndex2,
int order)
|
(package private) Bond |
addNewBond(java.lang.String atomName1,
java.lang.String atomName2)
|
Bond |
addNewBond(java.lang.String atomName1,
java.lang.String atomName2,
int order)
|
Bond |
addNewBondWithMappedSerialNumbers(int atomSerial1,
int atomSerial2,
int order)
|
(package private) boolean |
addSpaceGroupOperation(java.lang.String xyz)
|
void |
addStructure(Structure structure)
|
(package private) void |
addTrajectory()
|
protected void |
appendAtomSetCollection(int collectionIndex,
AtomSetCollection collection)
Appends an AtomSetCollection |
private void |
appendAtomSetCollection(java.util.Vector list)
|
private void |
applyAllSymmetry(int maxX,
int maxY,
int maxZ)
|
(package private) void |
applySymmetry()
|
(package private) void |
applySymmetry(int maxX,
int maxY,
int maxZ)
|
(package private) void |
applySymmetry(SymmetryInterface symmetry)
|
void |
applySymmetry(java.util.Vector biomts,
boolean applySymmetryToBonds,
java.lang.String filter)
|
private void |
clearSymbolicMap()
|
(package private) void |
cloneAtomSetProperties(int index)
Clones the properties of an atom set and associated it with the current atom set. |
void |
cloneFirstAtomSet()
|
void |
cloneFirstAtomSetWithBonds(int nBonds)
|
void |
cloneLastAtomSet()
|
void |
cloneLastAtomSetProperties()
Clones the properties of the last atom set and associates it with the current atom set. |
void |
connectAll(int maxSerial)
|
void |
createAtomSerialMap()
|
void |
discardPreviousAtoms()
|
(package private) void |
finalizeTrajectories()
|
(package private) void |
finish()
|
(package private) void |
freeze()
|
(package private) void |
getAltLocLists()
|
Atom |
getAtom(int i)
|
int |
getAtomCount()
|
int |
getAtomNameIndex(java.lang.String atomName)
|
Atom[] |
getAtoms()
|
int |
getAtomSerialNumberIndex(int serialNumber)
|
(package private) java.util.Hashtable |
getAtomSetAuxiliaryInfo(int atomSetIndex)
|
(package private) java.lang.Object |
getAtomSetAuxiliaryInfo(int index,
java.lang.String key)
|
java.lang.Object |
getAtomSetCollectionAuxiliaryInfo(java.lang.String key)
|
(package private) java.lang.String |
getAtomSetCollectionProperty(java.lang.String key)
|
int |
getAtomSetCount()
|
(package private) java.lang.String |
getAtomSetName(int atomSetIndex)
|
(package private) int |
getAtomSetNumber(int atomSetIndex)
|
(package private) java.util.Properties |
getAtomSetProperties(int atomSetIndex)
|
Bond |
getBond(int i)
|
int |
getBondCount()
|
Bond[] |
getBonds()
|
int |
getCurrentAtomSetIndex()
|
int |
getFirstAtomSetAtomCount()
|
(package private) void |
getInsertionLists()
|
int |
getLastAtomSetAtomCount()
|
int |
getLastAtomSetAtomIndex()
|
private SymmetryInterface |
getSymmetry()
|
java.lang.Object |
getVolumeData()
|
(package private) boolean |
hasAlternateLocations()
|
(package private) boolean |
hasInsertions()
|
private boolean |
isInSymmetryRange(javax.vecmath.Point3f c)
|
(package private) void |
mapAtomName(java.lang.String atomName,
int atomIndex)
|
(package private) void |
mapMostRecentAtomName()
|
(package private) void |
mapMostRecentAtomSerialNumber()
|
void |
mapPartialCharge(java.lang.String atomName,
float charge)
|
void |
newAtomSet()
|
(package private) Atom |
newCloneAtom(Atom atom)
|
void |
newVolumeData()
|
void |
removeAtomSet()
|
(package private) void |
setApplySymmetryToBonds(boolean TF)
|
java.util.Properties |
setAtomNames(java.util.Properties atomIdNames)
|
void |
setAtomSetAuxiliaryInfo(java.lang.String key,
java.lang.Object value)
Sets auxiliary information for the AtomSet |
(package private) void |
setAtomSetAuxiliaryInfo(java.lang.String key,
java.lang.Object value,
int atomSetIndex)
Sets auxiliary information for the an AtomSet |
void |
setAtomSetCollectionAuxiliaryInfo(java.lang.String key,
java.lang.Object value)
|
boolean |
setAtomSetCollectionPartialCharges(java.lang.String auxKey)
Sets the partial atomic charges based on atomSetCollection auxiliary info |
void |
setAtomSetCollectionProperty(java.lang.String key,
java.lang.String value)
Sets a property for the AtomSetCollection |
void |
setAtomSetName(java.lang.String atomSetName)
Sets the name for the current AtomSet |
void |
setAtomSetName(java.lang.String atomSetName,
int atomSetIndex)
Sets the name for an AtomSet |
void |
setAtomSetNames(java.lang.String atomSetName,
int n)
Sets the atom set names of the last n atomSets |
void |
setAtomSetNumber(int atomSetNumber)
Sets the number for the current AtomSet |
(package private) boolean |
setAtomSetPartialCharges(java.lang.String auxKey)
Sets the partial atomic charges based on atomSet auxiliary info |
void |
setAtomSetProperties(java.lang.String key,
java.lang.String value,
int n)
Sets the same properties for the last n atomSets. |
void |
setAtomSetProperty(java.lang.String key,
java.lang.String value)
Sets a property for the AtomSet |
void |
setAtomSetProperty(java.lang.String key,
java.lang.String value,
int atomSetIndex)
Sets the a property for the an AtomSet |
(package private) void |
setAtomSetSpaceGroupName(java.lang.String spaceGroupName)
|
void |
setCheckSpecial(boolean TF)
|
void |
setCollectionName(java.lang.String collectionName)
|
(package private) void |
setCoordinatesAreFractional(boolean coordinatesAreFractional)
|
void |
setFileTypeName(java.lang.String type)
Just sets the overall file type after the fact. |
(package private) void |
setGlobalBoolean(int globalIndex)
|
(package private) void |
setLatticeCells(int[] latticeCells,
boolean applySymmetryToBonds)
|
void |
setLatticeParameter(int latt)
|
(package private) void |
setNoAutoBond()
|
(package private) boolean |
setNotionalUnitCell(float[] info)
|
private void |
setSymmetryMinMax(javax.vecmath.Point3f c)
|
(package private) void |
setSymmetryRange(float factor)
|
(package private) boolean |
setTrajectory()
|
void |
setVolumetricOrigin(float x,
float y,
float z)
|
void |
setVolumetricVector(int i,
float x,
float y,
float z)
|
void |
setVoxelCounts(int nPointsX,
int nPointsY,
int nPointsZ)
|
void |
setVoxelData(float[][][] voxelData)
|
private int |
symmetryAddAtoms(int iAtomFirst,
int noSymmetryCount,
int transX,
int transY,
int transZ,
int baseCount,
int pt,
int iCellOpPt)
|
Methods inherited from class java.lang.Object |
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clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
Field Detail |
---|
java.lang.String fileTypeName
java.lang.String collectionName
java.util.Properties atomSetCollectionProperties
java.util.Hashtable atomSetCollectionAuxiliaryInfo
static final java.lang.String[] globalBooleans
static final int GLOBAL_FRACTCOORD
static final int GLOBAL_SYMMETRY
static final int GLOBAL_latticeCells
public static final java.lang.String[] notionalUnitcellTags
int atomCount
Atom[] atoms
int bondCount
Bond[] bonds
int structureCount
Structure[] structures
int atomSetCount
int currentAtomSetIndex
int[] atomSetNumbers
java.lang.String[] atomSetNames
int[] atomSetAtomCounts
int[] atomSetBondCounts
java.util.Properties[] atomSetProperties
java.util.Hashtable[] atomSetAuxiliaryInfo
int[] latticeCells
public java.lang.String errorMessage
boolean coordinatesAreFractional
boolean isTrajectory
int nTrajectories
javax.vecmath.Point3f[] trajectory
java.util.Vector trajectories
float[] notionalUnitCell
private boolean noAutoBond
java.util.Vector vConnect
int connectNextAtomIndex
int connectNextAtomSet
int[] connectLast
float symmetryRange
SymmetryInterface symmetry
boolean doNormalize
boolean isLatticeRange
private float rminx
private float rminy
private float rminz
private float rmaxx
private float rmaxy
private float rmaxz
javax.vecmath.Point3f[] cartesians
int bondCount0
int bondIndex0
boolean applySymmetryToBonds
boolean checkSpecial
private final javax.vecmath.Point3f ptTemp
private final javax.vecmath.Point3f ptTemp1
private final javax.vecmath.Point3f ptTemp2
java.util.Hashtable atomSymbolicMap
boolean haveMappedSerials
VolumeDataInterface vd
Constructor Detail |
---|
public AtomSetCollection(java.lang.String fileTypeName)
public AtomSetCollection(AtomSetCollection[] array)
array
- Array of AtomSetCollectionpublic AtomSetCollection(java.util.Vector list)
list
- Vector of AtomSetCollectionMethod Detail |
---|
public int getAtomCount()
public Atom[] getAtoms()
public Atom getAtom(int i)
public int getBondCount()
public Bond[] getBonds()
public Bond getBond(int i)
public int getAtomSetCount()
public int getCurrentAtomSetIndex()
private void appendAtomSetCollection(java.util.Vector list)
public void setFileTypeName(java.lang.String type)
type
- boolean setTrajectory()
protected void appendAtomSetCollection(int collectionIndex, AtomSetCollection collection)
collectionIndex
- collection index for new model numbercollection
- AtomSetCollection to appendvoid setNoAutoBond()
void finish()
void freeze()
public void discardPreviousAtoms()
public void removeAtomSet()
Atom newCloneAtom(Atom atom) throws java.lang.Exception
java.lang.Exception
public void cloneFirstAtomSet() throws java.lang.Exception
java.lang.Exception
public void cloneFirstAtomSetWithBonds(int nBonds) throws java.lang.Exception
java.lang.Exception
public void cloneLastAtomSet() throws java.lang.Exception
java.lang.Exception
public int getFirstAtomSetAtomCount()
public int getLastAtomSetAtomCount()
public int getLastAtomSetAtomIndex()
public Atom addNewAtom()
public void addAtom(Atom atom)
public void addAtomWithMappedName(Atom atom)
public void addAtomWithMappedSerialNumber(Atom atom)
public Bond addNewBond(int atomIndex1, int atomIndex2)
Bond addNewBond(java.lang.String atomName1, java.lang.String atomName2)
public Bond addNewBond(int atomIndex1, int atomIndex2, int order)
public Bond addNewBond(java.lang.String atomName1, java.lang.String atomName2, int order)
public Bond addNewBondWithMappedSerialNumbers(int atomSerial1, int atomSerial2, int order)
public void addConnection(int[] is)
public void connectAll(int maxSerial)
public void addBond(Bond bond)
public void addStructure(Structure structure)
void setAtomSetSpaceGroupName(java.lang.String spaceGroupName)
void setCoordinatesAreFractional(boolean coordinatesAreFractional)
void setSymmetryRange(float factor)
void setLatticeCells(int[] latticeCells, boolean applySymmetryToBonds)
private SymmetryInterface getSymmetry()
boolean setNotionalUnitCell(float[] info)
void setGlobalBoolean(int globalIndex)
boolean addSpaceGroupOperation(java.lang.String xyz)
public void setLatticeParameter(int latt)
void applySymmetry() throws java.lang.Exception
java.lang.Exception
void applySymmetry(SymmetryInterface symmetry) throws java.lang.Exception
java.lang.Exception
void applySymmetry(int maxX, int maxY, int maxZ) throws java.lang.Exception
java.lang.Exception
private void setSymmetryMinMax(javax.vecmath.Point3f c)
private boolean isInSymmetryRange(javax.vecmath.Point3f c)
private void applyAllSymmetry(int maxX, int maxY, int maxZ) throws java.lang.Exception
java.lang.Exception
public void setCheckSpecial(boolean TF)
void setApplySymmetryToBonds(boolean TF)
private int symmetryAddAtoms(int iAtomFirst, int noSymmetryCount, int transX, int transY, int transZ, int baseCount, int pt, int iCellOpPt) throws java.lang.Exception
java.lang.Exception
public void applySymmetry(java.util.Vector biomts, boolean applySymmetryToBonds, java.lang.String filter)
public void setCollectionName(java.lang.String collectionName)
void mapMostRecentAtomName()
private void clearSymbolicMap()
void mapMostRecentAtomSerialNumber()
public void createAtomSerialMap()
void mapAtomName(java.lang.String atomName, int atomIndex)
public int getAtomNameIndex(java.lang.String atomName)
public int getAtomSerialNumberIndex(int serialNumber)
public void setAtomSetCollectionProperty(java.lang.String key, java.lang.String value)
key
- The poperty key.value
- The property value.java.lang.String getAtomSetCollectionProperty(java.lang.String key)
public void setAtomSetCollectionAuxiliaryInfo(java.lang.String key, java.lang.Object value)
public boolean setAtomSetCollectionPartialCharges(java.lang.String auxKey)
auxKey
- The auxiliary key name that contains the charges
public void mapPartialCharge(java.lang.String atomName, float charge)
public java.lang.Object getAtomSetCollectionAuxiliaryInfo(java.lang.String key)
void addTrajectory()
void finalizeTrajectories()
public void newAtomSet()
public void setAtomSetName(java.lang.String atomSetName)
atomSetName
- The name to be associated with the current AtomSetpublic void setAtomSetName(java.lang.String atomSetName, int atomSetIndex)
atomSetName
- The number to be associated with the AtomSetatomSetIndex
- The index of the AtomSet that needs the associationpublic void setAtomSetNames(java.lang.String atomSetName, int n)
atomSetName
- The namen
- The number of last AtomSets that need these setpublic void setAtomSetNumber(int atomSetNumber)
atomSetNumber
- The number for the current AtomSet.public void setAtomSetProperty(java.lang.String key, java.lang.String value)
key
- The key for the propertyvalue
- The value to be associated with the keypublic void setAtomSetAuxiliaryInfo(java.lang.String key, java.lang.Object value)
key
- The key for the propertyvalue
- The value to be associated with the keyboolean setAtomSetPartialCharges(java.lang.String auxKey)
auxKey
- The auxiliary key name that contains the charges
java.lang.Object getAtomSetAuxiliaryInfo(int index, java.lang.String key)
public void setAtomSetProperty(java.lang.String key, java.lang.String value, int atomSetIndex)
key
- The key for the propertyvalue
- The value for the propertyatomSetIndex
- The index of the AtomSet to get the propertyvoid setAtomSetAuxiliaryInfo(java.lang.String key, java.lang.Object value, int atomSetIndex)
key
- The key for the propertyvalue
- The value for the propertyatomSetIndex
- The index of the AtomSet to get the propertypublic void setAtomSetProperties(java.lang.String key, java.lang.String value, int n)
key
- The key for the propertyvalue
- The value of the propertyn
- The number of last AtomSets that need these setpublic void cloneLastAtomSetProperties()
void cloneAtomSetProperties(int index)
index
- The index of the atom set whose properties are to be cloned.int getAtomSetNumber(int atomSetIndex)
java.lang.String getAtomSetName(int atomSetIndex)
java.util.Properties getAtomSetProperties(int atomSetIndex)
java.util.Hashtable getAtomSetAuxiliaryInfo(int atomSetIndex)
boolean hasAlternateLocations()
void getAltLocLists()
boolean hasInsertions()
void getInsertionLists()
public void newVolumeData()
public void setVoxelCounts(int nPointsX, int nPointsY, int nPointsZ)
public void setVolumetricVector(int i, float x, float y, float z)
public void setVolumetricOrigin(float x, float y, float z)
public void setVoxelData(float[][][] voxelData)
public java.lang.Object getVolumeData()
public java.util.Properties setAtomNames(java.util.Properties atomIdNames)
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